diff frogsfunc_pathways.xml @ 9:7bf54edaba24 draft

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 3d595459e82ea1674c83543f41c18169c159450e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/frogsfunc_pathways.xml	Thu May 12 10:44:30 2022 +0000
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+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2022 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGSFUNC_step4_pathways" name="FROGSFUNC_step4_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+	<description>Inference of pathway-level abundances. </description>
+
+  <macros>
+        <import>macros.xml</import>
+  </macros>
+
+  <expand macro="requirements_frogsfunc" />
+
+  <stdio>
+    <exit_code range="1:" />
+    <exit_code range=":-1" />
+  </stdio>
+	<command >   
+       frogsfunc_pathways.py
+          --input-file $input_file
+          #if $normalisation
+            --normalisation
+          #end if
+	    --map $map_file.value
+         
+          #if $category.value == "16S"
+            #if $map_file.fields.name == "Kegg"
+             --no-regroup
+            #end if
+          #end if
+	    --html $summary_file
+	</command> 
+	<inputs>
+        <!-- Input files -->       
+        <param argument="--input-file" format="tabular" name="input_file" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table)." optional="false"/>
+
+        <!-- References -->
+	      <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio">
+          <options from_data_table="frogs_picrust2_pathway_map">
+            <column name='name' index='2' />
+            <column name='value' index='2' />
+            <filter type="unique_value" column='2'/>
+              <validator type="no_options" message="A built-in database is not available" />
+          </options>
+			  </param>
+        <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'>
+          <options from_data_table="frogs_picrust2_pathway_map">
+            <column name='name' index='1'/>
+            <column name='value' index='3'/>
+            <filter type="param_value" ref="category" column="2" />               
+              <validator type="no_options" message="A built-in database is not available" />
+          </options>
+        </param>
+
+        <!-- Parameters-->
+        <param argument="--normalisation" label="Do you want to normalize the final output table ?" help='Values are divided by sum of columns, then multiplied by 10^6 (CPM values).' type="boolean" />
+        </inputs>
+	<outputs>
+		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
+		 <data format="tabular" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> 
+	</outputs>
+
+  <tests>
+    <test>
+      <param name="input_file" value="input/frogsfunc_functions_unstrat.tsv" />
+      <param name="category" value="16S" />
+
+      <output name="abund" file="references/28-frogsfunc_pathways_unstrat.tsv" compare="diff" lines_diff="0" />
+      <output name="summary_file" file="references/28-frogsfunc_pathways_report.html" compare="diff" lines_diff="0" />
+    </test>
+  </tests>
+
+     <help>
+
+@HELP_LOGO@
+
+.. class:: infomark page-header h2
+	     
+What it does
+
+FROGSFUNC_step4_pathway is the last step of `PICRUSt2 &lt;https://github.com/picrust/picrust2&gt;`_. This script infers MetaCyc/KEGG pathway abundances based on EC/KO number abundances.
+	     
+    - Regroups EC/KO numbers to MetaCyc/KEGG reactions.
+    - Infers which MetaCyc/KEGG pathways are present based on these reactions with `MinPath &lt;http://omics.informatics.indiana.edu/MinPath/&gt;`_.
+    - Calculates and returns the abundance of pathways identified as present.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**Function prediction abundance file**:
+
+ TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table).
+
+**Taxonomic marker:**
+
+ Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_step2_copynumbers tool. (frogsfunc_copynumbers_marker.tsv)
+
+**Pathway reference:**
+
+ Mapping of pathways to reactions.
+ 
+ - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. If you want both, run this tool twice.
+ - For ITS or 18S marker, Metacyc is the only valid option.
+
+
+**Do you want to normalize the final output table ?**:
+ 
+ If this option is set, the pathway abundances file (frogsfunc_functions_unstrat.tsv) is normalized: values are divided by sum of columns, then multiplied by 10^6 (Count Per Million values).
+
+.. image:: icon_warning_sml.gif 
+
+This normalization allows to compare the samples between them. But to perform more precise statistical analysis, some tools as **DESeq2 need the non-normalized abundance table** to perform the normalization by themselves. So be careful which table to use for further analysis.
+
+.. class:: h3
+
+Outputs
+
+**HTML report**:        
+ 
+ The HTML file summarizes information about pathway abundances within each sample.
+ 
+.. image:: FROGS_frogsfunc_pathways_sunburst.png
+
+
+
+
+**Pathways abundances tables - unstratified**:
+
+ It is the pathways abundance predictions of metagenome, per sample. (frogsfunc_pathways_unstrat.tsv)
+
+ - Classification column: the hierarchy classification of the pathway.
+ - db_link column: the url on the link accession ID (observation_name) of the pathway.
+ - observation_name: Accession identifier
+ - last columns: Abundances of these pathway in each samples.
+
+
+
+
+@HELP_CONTACT@
+
+  </help>
+
+  <expand macro="citations" />
+  
+</tool>